Genome Biology And Evolution[JOURNAL]
Sun
200 papers
The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.
Klemp FL, Hörandl E, Maraun M … +2 more , Scheu S, Heimburger B
Genome Biol Evol · 2026 May · PMID 41967468 · Full text
With the increasing availability of whole-genome assemblies, interest in the genomic consequences of diverse reproductive modes has grown. Reduced efficiency of selection in asexually reproducing species is often cited a...
With the increasing availability of whole-genome assemblies, interest in the genomic consequences of diverse reproductive modes has grown. Reduced efficiency of selection in asexually reproducing species is often cited as a major consequence and is frequently investigated using the ratio of nonsynonymous to synonymous substitutions (dN/dS). However, many studies do not give sufficient attention to the fundamental differences between nonsexual reproductive modes, which likely have substantial effects on the efficiency of selection. We reviewed studies that compared dN/dS ratios of sexual and asexual relatives across 20 taxa. Asexual reproductive modes were classified into two categories: Meiosis without interchromosomal mixis (automixis and premeiotic doubling), i.e. modified meiosis that restores ploidy without outcrossing, and apomixis, i.e. production of unreduced eggs that develop without meiosis and without interchromosomal or intrachromosomal mixis. We further included two modes of reproduction which are not sexual and not strictly asexual, but may be seen as such at first glance: Fissiparity/clonal growth, i.e. the formation of new modules/ramets by splitting of somatic tissue without meiosis or mixis, and selfing, i.e. meiosis followed by fertilization of the gametes by the same individual. Consistent with theory, fissiparous lineages generally exhibited elevated dN/dS ratios, whereas automicts and apomicts showed no consistent pattern, even among taxa with identical reproductive modes. We discuss limitations of commonly used phylogenetic analyses using maximum likelihood (PAML) branch and branch-site models, which can obscure subtle differences, and propose different avenues to assess detection of selection. We propose that the heterogeneous patterns in asexual lineages reflect lineage-specific consequences of asexuality, model limitations, and our incomplete understanding of cytological mechanisms underlying different nonsexual reproductive modes.
Big Spider, Big Genome: Chromosome-Level Genome of a North American Tarantula (Aphonopelma marxi) and Comparative Genomics Across 300 Million Years of Spider Evolution.
Briggs EJ, Noble-Stuen AJ, Hamilton CA
Genome Biol Evol · 2026 Apr · PMID 41964425 · Full text
The comparison of chromosome-level genomes allows biologists to investigate new axes of organismal evolution. Spiders comprise a significant proportion of known arachnid diversity, with many complex morphologies and uniq...
The comparison of chromosome-level genomes allows biologists to investigate new axes of organismal evolution. Spiders comprise a significant proportion of known arachnid diversity, with many complex morphologies and unique natural histories, yet comparative genomics in spiders has been limited due to the number of available genomes. We present a de novo chromosomal reference genome of a mature male tarantula, Aphonopelma marxi, and comparatively examine spider genome evolution across the order Araneae. Using PacBio HiFi and Hi-C sequencing, the final 6.5 Gb assembly consists of 17 autosomes, 1 X chromosome, and 127 unplaced scaffolds, with an N50 of 370 Mb and Arachnida (odb10; 2,934 genes) BUSCO of 96.7%. By comparing 20 additional spider genomes from 15 families, we find mygalomorphs (trapdoor spiders and their kin) generally possess more repetitive genomes with similar composition compared to their much more diverse sister lineage, the araneomorphs. We report mygalomorphs recover a lower number of completed BUSCOs than araneomorph spiders, a finding not correlated with sequencing coverage, as mygalomorphs have a portion of missing or derived BUSCOs in the current arachnid dataset. Across the Araneoidea (orb-weaving spiders and their kin), there is a correlation between decreasing genome size and repeat content, suggesting repetitive elements are being lost or removed. Importantly, visualization of macrosynteny across available genomes highlights structural rearrangements and allows identification of previously unreported sex chromosomes. This new, high-quality mygalomorph genome will provide new avenues of exploration for arachnid evolutionary biology.
Empirical Validation of the Nearly Neutral Theory at Divergence and Population-Genomic Scales Using 144 Placental Mammal Genomes.
Bastian M, Enard D, Lartillot N
Genome Biol Evol · 2026 Apr · PMID 41936401 · Full text
By limiting the efficacy of selection, random drift is expected to play a major role in genome evolution. Formalizing this idea, the nearly-neutral theory predicts that the ratio of non-synonymous over synonymous polymor...
By limiting the efficacy of selection, random drift is expected to play a major role in genome evolution. Formalizing this idea, the nearly-neutral theory predicts that the ratio of non-synonymous over synonymous polymorphism (πN/πS) within populations, and divergence (dN/dS) between species, should both correlate negatively with Ne. This has previously been tested in mammals and other groups. However, most studies have focused on either dN/dS or on πN/πS, thus not addressing the problem across evolutionary scales. In addition, many studies at the macro scale have used life-history traits (LHT) as a proxy of Ne, assuming that large-bodied organisms have lower Ne than small-bodied species. However, this assumption itself has rarely been validated against more objective measures of Ne, such as genetic diversity πS=4Neμ, in part because πS estimates are scarce. Here we propose an integrative test of the nearly-neutral predictions on 150 mammalian species, using 6000 orthologous genes, spanning the macro and the micro-evolutionary scale, using for the latter a measure of heterozygosity on each of the assembled diploid genomes. At the micro scale, we observe, for the first time in mammalian nuclear genomes, a relationship between πN/πS and πS. At the macro scale, we confirm the positive correlation between dN/dS and LHT but, more importantly, establish that LHT and dN/dS are correlated with πS, although weakly so. Together, these results provide the first global test of the nearly-neutral theory in mammals across time scales, suggesting all variables are correlated with a single hidden variable: Ne.
Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life.
Chantzi N, Moeckel C, Chan CSY … +6 more , Nayak A, Wang G, Mouratidis I, Chartoumpekis D, Vasquez KM, Georgakopoulos-Soares I
Genome Biol Evol · 2026 May · PMID 41934469 · Full text
Inverted repeats (IRs) can form alternative DNA secondary structures, including hairpins and cruciforms, which have a multitude of functional roles and have been associated with genomic instability. However, their preval...
Inverted repeats (IRs) can form alternative DNA secondary structures, including hairpins and cruciforms, which have a multitude of functional roles and have been associated with genomic instability. However, their prevalence across diverse organismal genomes remains only partially understood. Here, we examine the prevalence of perfect IRs, which do not have mismatches in their arms, across 118,019 complete organismal genomes. Our comprehensive analysis across taxonomic subdivisions reveals significant differences in the distribution, frequency, and biophysical properties of perfect IRs among these genomes. We identify a total of 33,558,920 perfect IRs and show a highly variable density across different organisms, with strikingly distinct patterns observed in Viruses, Bacteria, Archaea, and Eukaryota. We report IRs with perfect arms of extreme lengths, which can extend to hundreds of thousands of base pairs. Our findings reveal that Bacteria possess the highest IR density. Additionally, this study reveals the enrichment of IRs at transcription start and end sites in prokaryotes and Viruses and underscores their potential roles in gene regulation and genome organization. Analysis of intraspecies variation shows elevated substitution burden in IR spacers and relative conservation of IR arms, particularly near transcriptional terminators. Through a comprehensive overview of the distribution and characteristics of IRs in a wide array of organisms, this largest-scale analysis to date sheds light on the functional significance of perfect IRs, their contribution to genomic instability, and their evolutionary impact across the tree of life.
Complex Patterns of Hitchhiking Mutation Load Among Stickleback Populations.
Nickel J, Laine J, Foote AD
Genome Biol Evol · 2026 Apr · PMID 41933904 · Full text
Positive selection causes beneficial alleles to rise to high frequency in a population. This can cause linked genetic variation to "hitchhike," and thereby also rise in frequency. This linked variation may include delete...
Positive selection causes beneficial alleles to rise to high frequency in a population. This can cause linked genetic variation to "hitchhike," and thereby also rise in frequency. This linked variation may include deleterious recessive alleles, previously neutrally harbored at low frequency and in heterozygous genotypes. Modeling studies have shown that local effective population size and reduced recombination rate should contribute to the probability of deleterious mutations being swept to high frequency by being linked to beneficial alleles in selective sweeps or selection on inversion karyotypes. Marine sticklebacks have repeatedly adapted to thousands of freshwater habitats that became available after the last ice age, resulting in the formation of distinct marine and freshwater ecotypes. Selection acts on ancient standing genetic variation present in marine populations, causing freshwater-adaptive alleles to increase rapidly over tens of generations. These genomic regions play a key role in the repeated freshwater adaptation of morphological, physiological, and behavioral traits, and evolve under strong selection. Thus, threespine stickleback is an ideal system for investigating the impact of hitchhiking mutation load. We estimate the mutation load in regions of low recombination, including inversions and the Eda haplotype. We find some evidence for increased accumulation of deleterious alleles in one inversion, while this is not the case for two other inversions. Inversions deviated from Hardy-Weinberg equilibrium in several populations due to an excess of homozygotes.
Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.
Amin MR, Arnab SP, Khan M … +1 more , DeGiorgio M
Genome Biol Evol · 2026 Apr · PMID 41928457 · Full text
A major challenge in population genomics is accurately identifying and characterizing natural selection from genomic data. The wide availability of dense whole-genome datasets has enabled researchers to analyze and local...
A major challenge in population genomics is accurately identifying and characterizing natural selection from genomic data. The wide availability of dense whole-genome datasets has enabled researchers to analyze and localize genetic variation within populations. Powerful supervised machine learning methods allow researchers to extract spatial information about genetic variation across the genome and identify traces of natural selection. While convolutional neural networks capture correlations among neighboring features, design choices such as heavy-pooling or limited receptive fields can lead to loss of fine-grained spatial resolution. Extensions like dilated convolutions or attention mechanisms mitigate this issue of loss of spatial resolution but at the cost of increased architectural complexity and parameter count when capturing correlations at different scales. In contrast, trend filtering directly models the autocovariation of neighboring features, ensuring that spatial relationships remain intact without any architectural extensions. When integrated into a classical machine learning model, such as a support vector machine, trend filtering offers a natural framework to create powerful predictive models while retaining the spatial integrity of the input. Here, we introduce SKINET, which employs a novel trend filter kernel within a support vector machine framework and apply it to the task of detecting and characterizing regions affected by positive natural selection. Specifically, SKINET not only distinguishes regions under positive natural selection from neutrally evolving regions but also functions in a regression framework to estimate associated adaptive parameters. Moreover, applying SKINET to empirical human genome variation identifies adaptive candidate genes consistent with previous findings while also uncovering novel adaptation targets, such as FAM177A1, that are linked to cancer.
Genetic Footprints of Seasonal Fluctuating Selection: A Comparison With Established Selection Forms.
Johnson OL, Tobler R, Schmidt JM … +1 more , Huber CD
Genome Biol Evol · 2026 Apr · PMID 41925020 · Full text
Fluctuating selection is frequently studied in natural populations by observing allele frequency trajectories over evolutionarily brief timeframes or through theoretical analyses of frequency dynamics. However, little is...
Fluctuating selection is frequently studied in natural populations by observing allele frequency trajectories over evolutionarily brief timeframes or through theoretical analyses of frequency dynamics. However, little is known of its effect on linked neutral diversity. Here, we simulate seasonally fluctuating selection at a single locus and characterize its genomic footprint using diversity, site-frequency spectrum (SFS), and haplotype-based statistics. We find that adaptively fluctuating loci exhibit distinct signals that depend on when in the seasonal cycle the population was sampled and whether sampling occurs early or late relative to the onset of the cyclic selection pressure. Compared with other modes of selection acting on a single locus, adaptively fluctuating loci show genomic signatures that are not shared by hard and soft selective sweeps but overlap considerably with heterozygote advantage. Leveraging linear discriminant analysis, we identify a combination of summary statistics that most effectively distinguish fluctuating selection from heterozygote advantage. Our findings shed light on the characteristic genomic signatures of fluctuating selection and imply that in-depth analyses of the long-term dynamics of adaptively fluctuating loci is achievable from sequence data collected from one or two time points across a selection cycle.
Evolutionary Complexity of Primate Immune System Uncovered by the Extensive Phylogenomic Sampling.
Zhang X, Wu B, Shao Y
Genome Biol Evol · 2026 Apr · PMID 41921952 · Full text
The immune system mediates the complex interaction between pathogenic microorganisms and their hosts. Despite its significance, the evolutionary mechanisms underlying immune system complexity in primates remain largely e...
The immune system mediates the complex interaction between pathogenic microorganisms and their hosts. Despite its significance, the evolutionary mechanisms underlying immune system complexity in primates remain largely elusive. In this study, we investigated the evolution of the primate immune system by generating the first comprehensive catalog of immune-related genes through extensive phylogenomic sampling. Our analyses uncovered substantial genetic diversity in the evolution of the primate immune system, in the form of modules that vary in their sequences and functional capabilities. We identified a novel module (Type 3c) that has experienced long-term coevolution between primates and lentiviruses over a long evolutionary timescale. Furthermore, we found that social system complexity, rather than diet or group size, may potentially shape the immune system evolution of primates. We further uncovered the evolutionary histories of key immune-associated genes, including IFNAR2 and C5AR1, which are implicated in SARS-CoV-2 infection. More importantly, we revealed a divergence in the selective pressures on immune-associated genes between experimental primates and humans. This finding provides a critical caveat, suggesting that extreme caution is warranted when using these primates as models for human diseases such as HIV-1, Hepatitis C, and Influenza A. In summary, this work uncovers key evolutionary mechanisms that have fundamentally shaped the complexity of immune systems across primates.
Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates.
Cai H, Des Marais DL
Genome Biol Evol · 2026 Apr · PMID 41914344 · Full text
Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. Nevertheless, the mechanisms influencing the probability of early duplicate retention an...
Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. Nevertheless, the mechanisms influencing the probability of early duplicate retention and the emergence of functional biases,such as the enrichment of tandem duplicates in environmental responses, remain unclear. Here, to elucidate the mechanisms and factors determining gene retention, we study a frequently overlooked molecular feature-within-line expression variation, termed expression variability. We demonstrate that, on average, genes with duplicates exhibit higher expression variability than singletons. Furthermore, small-scale duplications (SSDs) and whole-genome duplications (WGDs) display contrasting functional outcomes and time-dependent profiles in expression variability. These findings suggest a potential overarching mechanism that facilitates gene expression divergence, functional gains of environmental responses, and duplicate retention following SSDs.
De Novo Chromosome-Level Assembly of the Endangered Pilocarpus Microphyllus Highlights Genomic Resources for Conservation and Sustainable Pilocarpine Extraction.
Sobreiro MB, Magalhães L, Argolo LA … +10 more , Nacif CL, Batista CEA, Cordeiro DM, Moreira-Oliveira RR, Oliveira G, Aleixo A, Carvalho CDS, Caldeira CF, Vilaça ST, Vidal AF
Genome Biol Evol · 2026 Mar · PMID 41885800 · Full text
Pilocarpus microphyllus (jaborandi) is an endangered plant species with significant bioeconomic relevance, as it is the main known source of pilocarpine, an alkaloid widely used in the treatment of glaucoma and other dis...
Pilocarpus microphyllus (jaborandi) is an endangered plant species with significant bioeconomic relevance, as it is the main known source of pilocarpine, an alkaloid widely used in the treatment of glaucoma and other diseases. Here, we present a functionally annotated, haplotype-phased, chromosome-level genome for P. microphyllus, combining PacBio HiFi and Hi-C sequencing. The final genome assembly spans 2.6 Gb anchored into 22 chromosomes across 95 scaffolds, with a scaffold N50 of 120.9 Mb and a BUSCO completeness score of 99.66%. We obtained 28,319 unique protein-coding loci, of which 28,090 were functionally annotated to the RefSeq database. Repetitive sequences constituted 88.98% of the total genome length. This near-T2T genome provides a robust molecular foundation for investigating the pilocarpine biosynthetic pathway and supports future population-level studies, thereby contributing to improved management and conservation strategies.
Structural Constraints Acting on the SARS-CoV-2 Spike Protein Reveal Limited Space for Viral Adaptation.
Herzig JC, Magwira ML, Lovell SC
Genome Biol Evol · 2026 Mar · PMID 41876430 · Full text
The SARS-CoV-2 pandemic resulted in an unprecedented scientific response. The scale of global genome sequencing, protein structural determination, and targeted studies of variant dynamics has resulted in a unique dataset...
The SARS-CoV-2 pandemic resulted in an unprecedented scientific response. The scale of global genome sequencing, protein structural determination, and targeted studies of variant dynamics has resulted in a unique dataset, providing a valuable resource for studying viral evolutionary dynamics. Previous analysis of SARS-CoV-2 evolution has revealed apparently saltatory dynamics, with viral variants arising following evolutionary jumps without genetic intermediates represented in the sequence database. We utilize rich SARS-CoV-2 datasets to interrogate the role of protein structural constraint in SARS-CoV-2 evolution and whether saltatory dynamics result from the spike protein accessing previously nonviable sequence space. We apply multiple computational predictors of structural constraint across different structural backgrounds and assess how constraint has changed during SARS-CoV-2 variant evolution. These predictions are validated using substitution data from the SARS-CoV-2 global sequence database. We find that the structural constraint experienced by specific sites has undergone limited change, despite significant phenotypic evolution of the SARS-CoV-2 S protein. The structural constraints acting on signature mutations of variants of concern remain constant regardless of which viral variant structure is used to make predictions. We also develop a machine learning model to assess substitution viability, combining predictors of evolutionary constraint with information about local structural context. This confirms our conclusions, with model performance largely unaffected by the use of different viral variant structures. These results suggest that despite its rapid rate of mutation, the SARS-CoV-2 S protein is subject to strict structural constraints and exhibited limited genomic plasticity following zoonotic transmission into the human population.
Genome Sequence Data Reveal Complex and Variable Ploidy in the Amoebozoan Acanthamoeba castellanii.
Colp MJ, Archibald JM
Genome Biol Evol · 2026 Apr · PMID 41876380 · Full text
Acanthamoeba castellanii is a free-living amoeba that is emerging as a model organism for the study of eukaryotic microbiology. This species is one of the most widely studied members of the Amoebozoa and is both an impor...
Acanthamoeba castellanii is a free-living amoeba that is emerging as a model organism for the study of eukaryotic microbiology. This species is one of the most widely studied members of the Amoebozoa and is both an important grazer in soil communities and an opportunistic human pathogen; A. castellanii is thus of evolutionary, ecological, and biomedical significance. Despite its potential as a lab workhorse, the genome biology of A. castellanii is complex and poorly understood. Polyploidy is a common feature of many amoebozoan genomes, and members of the genus Acanthamoeba are no exception; they appear to be not only polyploid, where genome copy number is inflated beyond the conventional haploid and diploid states, but also aneuploid, i.e. with inter-chromosomal copy number variation. To better understand aneuploidy in A. castellanii and how it may vary over time and between closely related strains, we analyzed nanopore and Illumina sequence datasets from several wild-type and mutant A. castellanii lines, with a focus on quantifying single nucleotide polymorphism and structural variant allele frequencies across chromosome-scale scaffolds. Sequence depth of coverage was also considered. Our findings suggest that intragenomic chromosome copy number is highly variable in Acanthamoeba, consistent with a considerable degree of aneuploidy, but is predominantly stable in laboratory culture and on the evolutionary scale of the species or genus.
Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus.
Christensen KE, Deal A, Wang JJ … +8 more , Duarte A, Edwards JL, Goodman JLN, Ma Z, Padilla SI, Szewczyk E, Rha C, Brem RB
Genome Biol Evol · 2026 Mar · PMID 41874284 · Full text
Organisms specialized to extreme environments can be the product of millions of years of evolutionary engineering and refinement. The underlying genetics can be quite distinct from those operating at earlier stages of tr...
Organisms specialized to extreme environments can be the product of millions of years of evolutionary engineering and refinement. The underlying genetics can be quite distinct from those operating at earlier stages of trait innovation. In this work, we have developed the multistress-resistant yeast Kluyveromyces marxianus, which diverged from its closest relative >20 million years ago, as a model for interspecies comparative biology and genomics. In growth assays of the Kluyveromyces genus, we found that K. marxianus exhibited unique tolerance of high heat and a subset of chemical stress conditions. We then generated and analyzed omic profiles from across the genus to find molecular features associated with-and potentially causal for-K. marxianus traits. Expression profiling revealed divergent lipid processing and membrane transport programs in K. marxianus, borne out in changes in lipid utilization in experimental assays. Sequence analyses found robust evidence for expansions in gene families in the K. marxianus genome, most notably among transmembrane transporters and in metabolic enzymes. In molecular-evolution tests, we identified adaptive protein variants throughout the K. marxianus genome, among which plasma membrane transporters were over-represented. These data enable a model of the molecular mechanisms and evolutionary pressures underlying K. marxianus traits, including adaptive changes to transporters, lipid processing, and membrane functions mediating stress resistance.
Evolutionary Dynamics of Gene Expression During Thermal Adaptation in Drosophila subobscura.
Antunes MA, Santos MA, Santos M … +2 more , Matos M, Simões P
Genome Biol Evol · 2026 Mar · PMID 41874283 · Full text
Global warming poses significant challenges to the persistence of biodiversity, requiring a deeper understanding of thermal adaptation, particularly at the genetic level. Examining gene expression changes offers critical...
Global warming poses significant challenges to the persistence of biodiversity, requiring a deeper understanding of thermal adaptation, particularly at the genetic level. Examining gene expression changes offers critical insight into the molecular mechanisms driving adaptation, helping to identify which genes are activated or repressed during the adaptive dynamics. This study investigates the evolutionary dynamics of gene expression in Drosophila subobscura populations from different origins under progressive warming conditions. By analyzing transcriptomic changes across two generation gaps (after 9 and 23 generations of evolution), we found some complex evolutionary patterns of gene expression, including shifts from up to downregulation and vice versa, with the population of Dutch origin exhibiting greater variability in adaptive response than the population of Portuguese origin. Such complex dynamics involved enrichment of DNA replication-and DNA repair mechanisms in particular-in both sets of populations, although the timing and direction differed between them. We also found consistent downregulation of the immunity-related toll-NF-κB pathway in the replicated populations derived from the Dutch population. This study documents the dynamic and shifting nature of gene expression during adaptation to warming environments and highlights the critical role of population's history in shaping adaptive strategies. These findings deepen our understanding of the transcriptomic mechanisms driving thermal adaptation and provide a basis for predicting evolutionary responses to climate change.
The Missing Piece: Functional Telomerase Restored in the Beetle Model.
Fajkus P, Štefanovie B, Závodník M … +4 more , Havlová K, Fojtová M, Peška V, Fajkus J
Genome Biol Evol · 2026 Mar · PMID 41873812 · Full text
The red flour beetle Tribolium castaneum yielded the first resolved telomerase reverse transcriptase structure but lacked a known telomerase RNA. We identify two telomerase RNA paralogs in Tribolium, confirm their expres...
The red flour beetle Tribolium castaneum yielded the first resolved telomerase reverse transcriptase structure but lacked a known telomerase RNA. We identify two telomerase RNA paralogs in Tribolium, confirm their expression, and reconstitute active telomerase in vitro. Extending this approach across Coleoptera, we detect telomerase RNA homologs in diverse beetle lineages, with conserved cores but lineage-specific template and telomeric DNA variants. Our findings establish Tribolium as a powerful model for telomerase biochemistry, illuminate the evolutionary plasticity of beetle telomere maintenance, and reveal a consistent lack of telomerase in several derived Scarabaeoidea subfamilies, pinpointing its evolutionary loss within this beetle clade.
Identifying Adaptive Footprints in the Presence of Demographic Uncertainty.
Arnab SP, Khan M, Campelo Dos Santos AL … +2 more , Fumagalli M, DeGiorgio M
Genome Biol Evol · 2026 Apr · PMID 41873523 · Full text
Identifying genomic regions shaped by natural selection is a central goal in evolutionary genomics. Existing machine learning methods for this task are typically trained on labeled data simulated according to specific ev...
Identifying genomic regions shaped by natural selection is a central goal in evolutionary genomics. Existing machine learning methods for this task are typically trained on labeled data simulated according to specific evolutionary scenarios. While effective in controlled settings, these models are limited by their reliance on explicit class labels, detecting only the processes they were trained to recognize. This limitation makes it difficult to interpret predictions for regions shaped by other evolutionary forces, a problem especially acute when analyzing genomes influenced by mixtures of adaptive and demographic factors. One-vs-rest strategies offer a potential alternative but suffer from the complexity of modeling processes as a catch-all "rest" class. Here, we explore positive-unlabeled learning as a flexible framework for detecting adaptive events. This semi-supervised approach permits identification of a target class using only positive labels and an unlabeled background, without requiring explicit modeling of negatives. To assess its utility, we focus on a binary classification setting for detecting selective sweeps against a mixed background of unlabeled sweeps and neutrally evolving regions. We introduce PULSe, a method that trains only on labeled sweep observations while treating remaining data as unlabeled. By avoiding assumptions about background composition, PULSe enables robust sweep discovery in realistic genomic landscapes. We evaluate performance across demographic, adaptive, and confounding contexts, including domain shift from misspecified models, and find that PULSe delivers strong generalizability. Finally, analyzing European and Bengali genomes, we recapitulate known sweep candidates, demonstrating PULSe as a versatile tool for detecting adaptive regions across diverse genomic landscapes.
Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.
Stephens TG, Kulczyk AW, Bhattacharya D
Genome Biol Evol · 2026 Apr · PMID 41873503 · Full text
Climate change has accelerated research on biodiverse coral reef ecosystems. However, this area of investigation is limited by our understanding of the biology of these organisms, with many of the genes identified as imp...
Climate change has accelerated research on biodiverse coral reef ecosystems. However, this area of investigation is limited by our understanding of the biology of these organisms, with many of the genes identified as important for stress response in corals being "dark," that is, with no ascribable biological function. To aid reverse genetic efforts, and help explore dark gene evolution in this lineage, we analyzed available genomic and transcriptomic data from corals with the goal of identifying well conserved (often lineage specific) dark gene families and interrogating their putative roles in coral biology using available multi-omics data and bioinformatic approaches. Many of the well conserved dark gene families are stress responsive, enriched in specific cell types, or have predicted 3D protein structures with significant similarity to known proteins that may be adaptive in corals. We demonstrate that dark genes form cosmopolitan (broadly shared) families which originated via bursts of lineage specific duplication, often involving genes with known functions. Analysis of single cell gene expression data suggests that dark gene provenance may have precipitated or been concomitant with the origin of novel coral functions such as biomineralization. Our results open a new window into coral evolution that integrates knowledge from known and dark genes to elucidate how these species achieved their remarkable success in diverse marine environments. The dark gene families we identified also provide a significant resource for future studies into the role of novel genes in coral biology and adaptation to climate change.
Regulatory RNA Patterns Associated with Bee Evolution Should Be Interpreted with Caution, but Correlational Studies Should Not Be Entirely Dismissed.
Brenman-Suttner D, Zayed A
Genome Biol Evol · 2026 Mar · PMID 41859943 · Full text
In this response to comments by Heneberg (2026) on our recent review, "The evolution of bees: insights from 'omic studies," we continue the scientific conversation about evidence linking RNA regulatory mechanisms to phen...
In this response to comments by Heneberg (2026) on our recent review, "The evolution of bees: insights from 'omic studies," we continue the scientific conversation about evidence linking RNA regulatory mechanisms to phenotypic traits. We acknowledge that studies connecting small noncoding RNAs and alternative splicing to social behavior phenotypes are largely correlational and should be interpreted with an appropriate level of caution. At the same time, we suggest that such findings may still offer valuable insights, given the hypothesized importance of regulatory mechanisms in social evolution and the substantial body of work in model organisms demonstrating causal links between these processes and phenotypic change.
Caution in Interpreting Regulatory RNA Associations With Eusocial Evolution in Bees.
Heneberg P
Genome Biol Evol · 2026 Mar · PMID 41858117 · Full text
Recent advances in transcriptomics and regulatory genomics have expanded interest in the potential roles of alternative splicing and noncoding RNAs in the evolution of eusociality in bees. A recently published review by...
Recent advances in transcriptomics and regulatory genomics have expanded interest in the potential roles of alternative splicing and noncoding RNAs in the evolution of eusociality in bees. A recently published review by Brenman-Suttner and Zayed synthesized this literature, highlighting numerous associations between the expression patterns of regulatory RNA and caste, task, and developmental states. However, there is a distinction between molecular associations and demonstrated causal roles in evolutionary processes, particularly for complex social traits. Drawing on established principles from evolutionary genomics and regulatory biology, we discuss the limitations of correlational transcriptomic data and highlight ongoing debates over the functional inference of circular RNAs and long noncoding RNAs. Clarifying these interpretive boundaries is essential for aligning conclusions with current evidence and for guiding future experimental research on the molecular basis of social evolution.
Response of Protein Coding Genes and microRNAs to Temperature Changes in Four Species of Drosophilids.
Tsang SSK, Nong W, Xie Y … +8 more , Qu Z, Yip HY, Diego Gaitan-Espitia J, Tai APK, Yeung YY, Tobe SS, Bendena WG, Hui JHL
Genome Biol Evol · 2026 Apr · PMID 41855143 · Full text
Insects are the most abundant described living animals in the world, and they play important roles in the environment and in human society. Climate change affects global biodiversity, and studying temperature-dependent e...
Insects are the most abundant described living animals in the world, and they play important roles in the environment and in human society. Climate change affects global biodiversity, and studying temperature-dependent effects on insects is relevant to understanding the impact of climate crisis. However, little is known relating to how climate affects gene expression in different sexes of insects. Here, we utilized four species of fruit flies Drosophila (D. melanogaster, D. virilis, D. pseudoobscura, and D. erecta), with the male and female flies of each species subjected to three different temperatures to test their gene expression responses. In the transcriptomic profiles of protein-coding genes and microRNAs generated in this study, we showed that under the same temperature, there are more male-biased than female-biased protein-coding genes and microRNAs in all four investigated drosophilid species. Interestingly, upon temperature changes, there were more differentially expressed protein-coding genes in females than males in all four investigated species, while the responses of microRNAs are highly species- and sexes-specific. This study showed that protein-coding genes and microRNAs have undergone different selection between sexes during drosophilids evolution.
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